(1 of )Cincinnati Bengals quarterback John Skelton stands on the sidelines during an NFL preseason football game against the Tennessee Titans, Saturday, Aug. 17, 2013, in Cincinnati. (AP Photo/Tom Uhlman)

Grant Cohn: John Skelton signing a huge development for the 49ers and here's why

SANTA CLARA – You think you know Jim Harbaugh, and then he goes and signs John Skelton as a backup quarterback.

Signing Skelton is a defining move of the Harbaugh Era. Not because Skelton is good. He isn't. He represents a dramatic shift in the 49ers' offensive philosophy.

Skelton does not fit into the offense the 49ers have run since Colin Kaepernick became the starting quarterback last season. Skelton can't run the read-option. He can't run, period. He's what scouts and coaches call "an iron deer on the lawn." He does not leave the pocket and when the pass rush closes in, he goes down. He is the least athletic quarterback of the Harbaugh Era.

"There are different levels of athleticism," said Harbaugh, "but anybody who plays quarterback in the National Football League is a pretty darn good athlete."

So, athletically, Skelton is at the "anybody" level.

Later, Skelton said in the locker room, "I'm fairly confident I'm not going to do the stuff Kap can do." The understatement of the season.

"Are you going to do more of the stuff Alex Smith did last year?" one reporter asked Skelton.

"Yeah, probably more like that," Skelton replied, and then he reconsidered. "Even him, he's probably more mobile than I am."

Skelton is honest. He also has a strong arm and he's tall – "good stature in the pocket," that's how Harbaugh described Skelton Wednesday afternoon.

Since when does Harbaugh care about stature in the pocket?

For two years he has been focusing on perimeter offense and the read-option, two things which do not require stature.

The 49ers acquired two shrimp quarterbacks this offseason, Colt McCoy in free agency and B.J. Daniels in the draft. Forget stature in the pocket, those two are peanuts in the pocket. But the 49ers wanted them because they can run.

Clearly, running recently plummeted down the list of things Harbaugh values in a quarterback and stature skyrocketed. And since stature is so important all of a sudden, McCoy and Daniels no longer can play in the style of offense the 49ers are going to run. That's why the 49ers cut B.J. Daniels Tuesday morning. The Seahawks, who still value mobility in their quarterbacks, signed Daniels about 24 hours later.

McCoy is still on the team but clearly has no future with the 49ers. Skelton probably will become the primary backup as soon as he learns the playbook.

What does all this mean? It means a lot. Harbaugh has changed his philosophy and priorities, nothing less.

It's a risk-reward thing.

There has been no reward this season running the read-option or the Pistol formation. The 49ers practiced those all offseason, clearly intending to base their offense around the threat of Kaepernick running. That would open up everything else, in theory.

But it hasn't worked out that way. Opposing defenses are all over the Pistol and the read-option. Practically every running play the 49ers have tried from the Pistol this season has gotten destroyed. Their running game works only when Kaepernick is under center. Frank Gore thrives when Kaepernick is under center.

The bigger issue is risk. Defenses are waiting to take shots at Kaepernick if he runs. The Packers took a shot at Kaepernick Week 1. The 49ers took a shot at Russell Wilson, a running quarterback, Week 2. That's how you defend dual-threat quarterbacks – knock them out of the game.

Look what happened to Robert Griffin III and the Redskins. Last season, their entire offense revolved around the Pistol and the read-option and Griffin running. What happened? He got hurt.

This season he hardly runs anymore. He looks like damaged goods. It's a shame.

And the Redskins are horrible. And Mike Shanahan looks like an irresponsible coach who ruined his franchise quarterback.

The 49ers don't want to be the Redskins. Harbaugh doesn't want to be Shanahan.

If you have a franchise quarterback, and Kaepernick is a franchise quarterback, you can't expose him each week to the kind of hits defensive ends and linebackers mete out. If Harbaugh does nothing else, he must protect the franchise quarterback.

Harbaugh understands all of this and after two bad early-season losses, he's had an epiphany.

Forget everything that happened last season. The Pistol and the read-option won't work as a base offense. Conventional offense is back. The 49ers now want their quarterbacks operating under center, handing the ball off to Frank Gore or standing in the pocket and throwing downfield to Vernon Davis and Anquan Boldin. That's what Kaepernick did last week against the Rams.

Call it Harbaugh Theory 2.0. That's why he got John Skelton.

<i>Grant Cohn writes sports columns and the "Inside the 49ers" blog for the Press Democrat's website. You can reach him at grantcohn@gmail.com.</i>